Not sure whether a decision that the students meet the NLRB's definition of employee means that they meet the same definition under IRS regulations. If it did, then sure, all private universities have failed to file W-2's for all of their scholarship athletes, the athletes have failed to pay income taxes. Many would owe penalties for their failure to file appropriate returns, withholding elections and FICA withholding. I'm not sure that one follows from the other though.
I'm also not certain whether the NLRB's decision necessarily extends to public non-profit institutions, rather than merely private non-profit institutions. It seemed they relied quite a bit on Northwestern's choice to extend scholarships to a 4 year duration, rather than just 1 year. Potential upshots of the decision may be that private non-profit institutions will only offer 1 year / temporary grant-in-aid programs (renewable at the whimsy of the head coach) or, if the NLRB's jurisdiction fails to extend to Public/State-owned/chartered Universities, that private universities are simply unable to be competitive anymore.
On a second point, the NCAA makes almost all of its money on March madness in basketball and very little on Football (check the leaked NCAA financial records to verify if you wish). The jerseys are a very unseemly and stupid mistake by the NCAA. Those sales are chump change compaired with the licensing & tv rights for the tournament that we're probably all watching. Control of football may matter, but it isn't a big source of revenue for the NCAA. The Ed O'Bannon lawsuit probably has them more concerned. They may beat the NU students on appeal within the NLRB and would certainly win before the DC Circuit (as long as republicans are able to prevent democratic appointees to fill vacancies on that circuit).